TCGA - Assembler : Pipeline for TCGA Data Downloading , Assembling , and Processing ( Supplementary Methods )

The Cancer Genome Atlas (TCGA) is supported by the National Cancer Institute and the National Human Genome Research Institute to chart the molecular landscape of tumor samples for more than 20 types of cancer [1-3]. TCGA has been generating multi-modal genomics, epigenomics, and proteomics data for thousands of cancer patients, providing unprecedented opportunities for researchers to systematically study cancer mechanisms at molecular and regulatory layers. There are different levels of data access for TCGA. While the access to most of the level-1 and -2 data is restricted, the entire level-3 TCGA data as well as some de-identified patient clinical information (e.g., survival and drug treatments) are publicly available. Level-3 TCGA data are normalized measurements of genomics and epigenomics features, e.g., DNA copy number, DNA methylation, mRNA expression, miRNA expression, and protein expression. Such a wealth of information enables biologists, clinicians, and quantitative geneticists to address various important research questions. For example, the level-3 data can be used to infer the effects of multiple types of transcriptional regulators, such as DNA methylation and transcription factors, on gene expression. This type of investigation requires matched data from multiple samples measured by all the relevant biological assays. We summarize the public TCGA data and report in Supplementary Table 1 the number of available samples measured by different assay platforms, and the numbers of patients with clinical information for the different cancer types.